Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate Ga0059261_0516 Ga0059261_0516 vanillin dehydrogenase (EC 1.2.1.67)
Query= BRENDA::P80668 (499 letters) >FitnessBrowser__Korea:Ga0059261_0516 Length = 478 Score = 248 bits (634), Expect = 3e-70 Identities = 169/476 (35%), Positives = 256/476 (53%), Gaps = 20/476 (4%) Query: 30 PAQSEKRLAIFDPATGQEIASTADANEADVDN-AVMSAWRAFVSRRWAGRLPAERERILL 88 P K A +P TG E+A+ A A D N AV +A AF + W+ P R L Sbjct: 6 PPAPGKTFARLNPVTG-EVATEAQAFTVDQANEAVEAAAAAFPA--WSTLGPNARRAALN 62 Query: 89 RFADLVEQHSEELAQLETLEQGKSIAISRAFEVGCTLNWMRYTAGLTTKIAGKTLDLSIP 148 + A+ + +E+ + E G + +R F + ++ +R A LTT+I G+ + P Sbjct: 63 KAAEALAAKAEDFVEAMNGEIGATEGWAR-FNLMLAVSMVREAAALTTQIGGEVIPSDKP 121 Query: 149 LPQGARYQAWTRKEPVGVVAGIVPWNFPLMIGMWKVMPALAAGCSIVIKPSETTPLTMLR 208 A +EPVGV+ GI PWN P+++G+ V LA G ++V+K SE P T Sbjct: 122 -----GCIAMAIREPVGVMLGIAPWNAPIILGVRAVAAPLACGNTVVLKASEQCPRTHSL 176 Query: 209 VAELASEAGIPDGVFNVVTGS---GAVCGAALTSHPHVAKISFTGSTATGKGIARTAADH 265 +AE EA +P G ++VT + AL +PH+ +I+FTGSTA G+ IA+ AA+H Sbjct: 177 IAEAFDEA-LPKGAVSIVTNAPEDAPEIVGALIDNPHIRRINFTGSTAVGRIIAKRAAEH 235 Query: 266 LTRVTLELGGKNPAIVLKDADPQWVIEGLMTGSFLNQGQVCAASSRIYIEAPLFDTLVSG 325 L V LELGGK P +VL+DAD ++ G+F+NQGQ+C ++ RI + + D V Sbjct: 236 LKPVLLELGGKAPMLVLEDADLDEAVKAAAFGAFMNQGQICMSTERIIVVDAVADAFVEK 295 Query: 326 FEQAVKSLQVGPGMSPVAQINPLVSRAHCDKVCSFLDDAQAQQAELIRGSNGPAGEGYYV 385 F V ++ VG + +V + V + + DA A A + G G G + Sbjct: 296 FAAKVGTMPVGDPREGKTPLGAVVDQKTVAHVKALIGDALAAGAVQVNGGGVLEGTGGVL 355 Query: 386 APTLV---VNPDAKLRLTREEVFGPVVNLVRVADGEEALQLANDTEYGLTASVWTQNLSQ 442 P V V PD ++L R+E FGPVV ++R D A+ LANDTEYGL+ASV+T++ ++ Sbjct: 356 MPAHVIDHVTPD--MKLFRDESFGPVVGVIRARDEAHAILLANDTEYGLSASVFTRDTAR 413 Query: 443 ALEYSDRLQAGTVWVNSHTLID-ANLPFGGMKQSGTGRDFGPDWLDGWCETKSVCV 497 L + ++++G VN T+ D A +PFGG+K SG GR G +D + E + + + Sbjct: 414 GLRVARQIKSGICHVNGPTVHDEAQMPFGGVKASGYGRFGGKAGIDAFTELRWITI 469 Lambda K H 0.318 0.133 0.402 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 560 Number of extensions: 26 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 499 Length of database: 478 Length adjustment: 34 Effective length of query: 465 Effective length of database: 444 Effective search space: 206460 Effective search space used: 206460 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory